diff --git a/changelogs/v4.7.1.md b/changelogs/v4.7.1.md index a620cca23..bd6ad757e 100644 --- a/changelogs/v4.7.1.md +++ b/changelogs/v4.7.1.md @@ -6,3 +6,4 @@ ## 📚 New Presets - Added preset `bruker-human-sc-xcr-vdj-beacon` for TCR/BCR analyses of Bruker Beacon data +- Added presets for new Qiagen kits: `qiagen-human-rna-tcr-umi-targeted-qiaseq` and `qiagen-mouse-rna-tcr-umi-targeted-qiaseq` \ No newline at end of file diff --git a/src/main/resources/presets/protocols/qiaseq.yaml b/src/main/resources/presets/protocols/qiaseq.yaml index 4b8c8c8e8..7e72cf28b 100644 --- a/src/main/resources/presets/protocols/qiaseq.yaml +++ b/src/main/resources/presets/protocols/qiaseq.yaml @@ -75,3 +75,47 @@ ^N{:4}gacacaaaggtatgtcccagtcttatggagatt(R1:*) | ^N{:4}ggaaaatagtaggcttgggagaaaagtctgagtc(R1:*) | ^N{:4}cacctctttagggtagaaatctttcaccagacaag(R1:*) \ ^(UMI:N{12})N{12}(R2:*) + + +"qiagen-human-rna-tcr-umi-targeted-qiaseq": + vendor: "QIAGEN" + label: "QIAseq Targeted RNA Panel Human TCR" + category: non-generic + inheritFrom: generic-amplicon-with-umi + pipeline: + - align + - refineTagsAndSort + - assemble + - exportClones + mixins: + - type: SetSpecies + species: hsa + - type: MaterialTypeRNA + - type: LeftAlignmentBoundaryNoPoint + floating: false + - type: RightAlignmentBoundaryNoPoint + floating: true + geneType: C + - type: SetClonotypeAssemblingFeatures + features: CDR3 + - type: AddQcChecks + args: + - type: OverlappedReadsLessBetter + middle: 0.05 + upper: 0.1 + - type: SetTagPattern + tagPattern: ^(R1:*) \ ^(UMI:N{14:18})atgcattggagtcct + align: + inheritFrom: generic-amplicon-with-umi + overrides: + parameters: + readsLayout: ReverseOnly + +"qiagen-mouse-rna-tcr-umi-targeted-qiaseq": + vendor: "QIAGEN" + label: "QIAseq Targeted RNA Panel Mouse TCR" + category: non-generic + inheritFrom: qiagen-human-rna-tcr-umi-targeted-qiaseq + mixins: + - type: SetSpecies + species: mmu \ No newline at end of file